Good post Mitch. In my posts on EAW in my series I covered his testimony where he said that his private investigation pointed to Duff being involved in the shooting.
The DPD initially thought Duff was enough of a suspect to arrest him. However, after questioning and a polygraph exam, he seems to have been cleared. The PIs that Walker's attorney hired to investigate Duff decided that the transplanted Scotsman was merely a con man and "a phony" but wasn't the shooter. Walker may well have believed Duff did the deed, but there's no evidence whatsoever for it.
When Duff had been cashiered from the Army (for enlistment fraud) and kicked out by his wife in early '64, it was Walker who secured a job and housing for Duff. I'm not entirely sure how to take that fact. Maybe it was a variation on the "keep your friends close and you enemies closer" meme. Providing employment and shelter for Duff allowed Walker, et al, to keep an eye on what Duff was up to. It certainly seems to have allowed Walker's PIs to sidle up to Duff. Or maybe Duff had something on Walker, and this was a way to keep Duff's mouth shut. There are other possibilities, I guess, all over the spectrum of suspicion.
What I got after going though the Walker/Duff material was a sudden, intuitive revelation: "Hey, Walker was gay!" I found out later that my intuition was correct.